Theory and Applications in Bioinformatics is a distance learning course
from the University of Manchester, UK. It will of interest to those who
need to gain confidence in the use of statistics for molecular
evolution. The course covers:

Introduction to Probability and Statistics using Matlab
Traditional Sequence Alignment and Search
Introduction to Probabilistic Sequence Models
Markov Chains and HMM Applications
Phylogenetic Methods

This is a Masters level course, so credits can count towards the MSc in
Bioinformatics.
(http://www.ls.manchester.ac.uk/postgraduate/distancelearning/).

The course is delivered in a Virtual Learning Environment, which allows
us to extend the classroom into the web. Teaching and learning are
focussed around tutor-supported exercises. Additional information is
available here :
http://octette.cs.man.ac.uk/bioinformatics/modules/bs6120.html or from
Heather.Vincent@manchester.ac.uk

Hi everybody!

Does anyone know (and recomend, of course) a free software or a web tool for primer design?

Thanks

Monica

___________________________________
Mônica Paiva Quast
Doutoranda/PhD Student
Laboratório de Macrobentos Marinho
Departamento de Zoologia, IB/UNICAMP - Brazil
+55 19 3521 6347

__________________________________________________________
Gesendet von Yahoo! Mail.
Dem pfiffigeren Posteingang.
http://de.overview.mail.yahoo.com

Hello,

I want to generate "random" alignment to use it as a neutral evolution
model for hypothesis testing. I need a phylogenetic tree of my species
for that.

I have used phylip package to generate a set of 1000 replicates, then I
have used PMB model to calculate the distances with protdist and finally
appllied neighbor and consese with default settings.

As a result a have an unrooted tree with bootstrap values generaly
better at the tips than in the center of the tree. In my understanding
this is a normal case, though some values are equal to 25%%.

So my question is what could I do with this tree? As I understand, 25%%
values emphasize the fact that different parts of distant sequnces do
not show consistency with overall comparison. I can not crop the
alignment. Should I use neighbor-joining to calculate the tree directly
from the alignment?
Thanks.

P.S. I have investigated 43 sequences with average length of 800 aa. The
consese tree is included.

+--------------------------------------------------------------------------------------------------------A4CHA4|A4C
|
|
+------A5V4S1|A5V
|
+---------------------364.0-|
...

The Agricultural Biotechnology International Conference is returning to
Europe this August and will be hosted by University College Cork in
Cork, Ireland. The annual ABIC conference brings many of the world's
largest agriculture, fisheries and food biotechnology companies to the
host country (many Fortune 500 companies) and this year is no exception.

At ABIC 2008 in Cork, there will be many hot topics under discussion and
debate including innovations in areas such as biofuels and bioenergy,
animal and plant breeding, fisheries biotech, molecular pharming, dairy
and food, including dedicated sessions on policy, regulatory affairs and
business strategies. Registration for the conference has now opened and
full details of ABIC 2008 are available on the conference website.
http://www.abic.ca/abic2008/html/program.html

The Agricultural
Biotechnology International Conference is returning to Europe this August and
will be hosted by University College Cork in Cork, Ireland.
The annual ABIC
conference brings many of the world's largest agriculture, fisheries and food
biotechnology companies to the host country (many Fortune 500 companies) and
this year is no exception.

Hi all -

I would like to offer my apology to Accelrys and its employees for
suggesting that the company would not follow through on their commitment
to supply non-node-locked, non-expiring license keys to all current GCG
custyomers with "perpetual" licenses. As I mentioned in my last posting
Accelrys is now involved in that process and I have received my new key.
It was never my intent to discredit Accelrys, nor its employess. I merely
had not been informed that the process was underway. I am sorry that I
miswrote and hope that any hard feelings can be overcome. Thank you.

Cheers - Steve
Steven M. Thompson
A C T G stevet@bio.fsu.edu
...

Hello all -

A brief note to let you know what's happened since my posting this last
Wednesday:

Rob Brown of Accelrys did contact me, finally. He says, and I quote:

"The petition and the subsequent BioInform article produced a significant
response and generated inquiries from a number of third party companies
who now wish to discuss various possibilities relating to GCG with us.
We are now in the process of following up on all of those which is taking
some time."

So, it looks like some good has come out of the process, although this
doesn't look like the open source type of arrangement that many of us
hoped for. Regardless, it may mean that the package will not be dying.

And, Accelrys sent me my new non-node-locked, non-expiring license key!

Cheers - Steve
Steven M. Thompson
A C T G stevet@bio.fsu.edu
...

Hi all - re. http://www.petitiononline.com/gcg/

A huge THANKS to all of you that signed my petition! Within the first
week online I got almost 150 signatures, and John Devereux himself most
recently signed it. I sent Rob Brown of Accelrys an 'official' copy of
the petition and the signatures at the end of last month. However, but
not surprisingly, I have yet to receive one word back from Accelrys. I
realize that we can't force them to do anything, but I at least thought
that they would have the courtesy to respond to it somehow. The petition
did result in a news story though. GenomeWeb News' bioinformatics
newsletter, BioInform, published the story on April 4th. See my copy at:

http://bio.fsu.edu/~stevet/BioInformGCG.pdf

Some may feel that the BioInform story suggests the petition was merely a
means of influencing commercial negotiations with Accelrys regarding code
release, and have nothing to do with public domain...

Hello,

This is a reminder that we will start reviewing applications for the
GMOD Summer School one week from today, on Wednesday, April 15. If
you are interested in attending then please submit a statement of
interest by the end of April 15.

See
http://gmod.org/GMOD_Summer_School and
http://gmod.org/GMOD_Summer_School_Statement_of_Interest

for more information.

Please let me know if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk

On Mon, Mar 24, 2008 at 1:32 PM, Dave Clements nescent.org> wrote:

Hi,

What I would like to to is to generate a phylogenetic tree based on 16s
sequences from 30 different bacteria plotted onto a larger tree showing
selected organisms from different prominent phyla. The idea is to
display the relationship between my 30 organisms AND how they relate to
the rest of the prokaryotes.

I used to this sort of thing by downloading each sequence from NCBI and
then align them and generate a phylogenetic tree in ClustalW or some
other software. I hope there exist some internet tools now that can do
it all for me, i.e. that I just select the species/strains and the
software retrives the sequences, aligns them and creates the tree
according to mye criteria. Do you know of any such sequences or do
people still do these kind of things "by hand"?

Regards,
Trond Erik

GMOD Summer School
11-13 July, 2008
National Evolutionary Synthesis Center (NESCent)
Durham, North Carolina, USA

The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will
be held July 11-13, 2008 at the National Evolutionary Synthesis Center
(NESCent), in Durham, North Carolina, USA. GMOD is a collection of
interoperable open source software components for managing genomic
data. GMOD components are used in diverse contexts, with both
emerging and established model organisms.

The course will provide an overview of GMOD and cover these popular
components in detail:
* Chado - a modular and extensible database schema
* Apollo - genome annotation editor
* GBrowse - genome viewer
* CMap - comparative map viewer
* Community Annotation System - GMOD's most popular components in a
single system